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Xu J, Yang KC, Go NE, Colborne S, Ho CJ, Hosseini-Beheshti E, Lystad AH, Simonsen A, Guns ET, Morin GB, Gorski SM. Chloroquine treatment induces secretion of autophagy-related proteins and inclusion of Atg8-family proteins in distinct extracellular vesicle populations. Autophagy 2022; 18:2547-2560. [PMID: 35220892 PMCID: PMC9629075 DOI: 10.1080/15548627.2022.2039535] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Chloroquine (CQ), a lysosomotropic agent, is commonly used to inhibit lysosomal degradation and macroautophagy/autophagy. Here we investigated the cell-extrinsic effects of CQ on secretion. We showed that lysosomal and autophagy inhibition by CQ altered the secretome, and induced the release of Atg8 orthologs and autophagy receptors. Atg8-family proteins, in particular, were secreted inside small extracellular vesicles (sEVs) in a lipidation-dependent manner. CQ treatment enhanced the release of Atg8-family proteins inside sEVs. Using full-length ATG16L1 and an ATG16L1 mutant that enables Atg8-family protein lipidation on double but not on single membranes, we demonstrated that LC3B is released in two distinct sEV populations: one enriched with SDCBP/Syntenin-1, CD63, and endosomal lipidated LC3B, and another that contains LC3B but is not enriched with SDCBP/Syntenin-1 or CD63, and which our data supports as originating from a double-membrane source. Our findings underscore the context-dependency of sEV heterogeneity and composition, and illustrate the integration of autophagy and sEV composition in response to lysosomal inhibition.Abbreviations: ACTB: actin beta; ANOVA: analysis of variance; ATG4B: autophagy related 4B cysteine peptidase; Atg8: autophagy related 8; ATG16L1: autophagy related 16 like 1; ATP5F1A/ATP5a: ATP synthase F1 subunit alpha; CALCOCO2: calcium binding and coiled-coil domain 2; CASP3: caspase 3; CASP7: caspase 7; CQ: chloroquine; CD9: CD9 molecule; CD63: CD63 molecule; DAPI: 4',6-diamidino-2-phenylindole; DQ-BSA: dye quenched-bovine serum albumin; ER: endoplasmic reticulum; ERN1/IRE1a: endoplasmic reticulum to nucleus signaling 1; EV: extracellular vesicles; FBS: fetal bovine serum; FDR: false discovery rate; GABARAP: GABA type A receptor-associated protein; GABARAPL2: GABA type A receptor associated protein like 2; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFP: green fluorescent protein; GO: gene ontology; HCQ: hydroxychloroquine; HSP90AA1: heat shock protein 90 alpha family class A member 1; IP: immunoprecipitation; KO: knockout; LAMP2: lysosomal associated membrane protein 2; LIR: LC3-interacting region; LMNA: lamin A/C; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MS: mass spectrometry; NBR1: NBR1 autophagy cargo receptor; NCOA4: nuclear receptor coactivator 4; NTA: nanoparticle tracking analysis; PE: phosphatidylethanolamine; PECA: probe-level expression change averaging; SDCBP/syntenin-1: syndecan binding protein; SD: standard deviation; SE: secreted; sEV: small extracellular vesicles; SQSTM1/p62: sequestosome 1; TAX1BP1: Tax1 binding protein 1; TEM: transmission electron microscopy; TMT: tandem-mass tag; TSG101: tumor susceptibility 101; ULK1: unc-51 like autophagy activating kinase 1; WC: whole cell.
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Affiliation(s)
- Jing Xu
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Kevin C Yang
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Nancy Erro Go
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Shane Colborne
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Cally J Ho
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Elham Hosseini-Beheshti
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney NSWAustralia
| | - Alf H Lystad
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Anne Simonsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway,Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, Norway
| | - Emma Tomlinson Guns
- The Vancouver Prostate Centre, Vancouver, BC, Canada,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Gregg B Morin
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Sharon M Gorski
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, BC, Canada,CONTACT Sharon M Gorski Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, Canada
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2
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Søreng K, Pankiv S, Bergsmark C, Haugsten EM, Dahl AK, de la Ballina LR, Yamamoto A, Lystad AH, Simonsen A. ALFY localizes to early endosomes and cellular protrusions to facilitate directional cell migration. J Cell Sci 2022; 135:274423. [PMID: 35099014 PMCID: PMC8919339 DOI: 10.1242/jcs.259138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/14/2022] [Indexed: 11/20/2022] Open
Abstract
Cell migration is a complex process underlying physiological and pathological processes such as brain development and cancer metastasis. The autophagy-linked FYVE protein (ALFY; also known as WDFY3), an autophagy adaptor protein known to promote clearance of protein aggregates, has been implicated in brain development and neural migration during cerebral cortical neurogenesis in mice. However, a specific role of ALFY in cell motility and extracellular matrix adhesion during migration has not been investigated. Here, we reveal a novel role for ALFY in the endocytic pathway and in cell migration. We show that ALFY localizes to RAB5- and EEA1-positive early endosomes in a PtdIns(3)P-dependent manner and is highly enriched in cellular protrusions at the leading and lagging edge of migrating cells. We find that cells lacking ALFY have reduced attachment and altered protein levels and glycosylation of integrins, resulting in the inability to form a proper leading edge and loss of directional cell motility. Summary: The autophagy-linked FYVE protein (ALFY) localizes to cell protrusions and early endosomes, and regulates directional cell migration and attachment by modification of integrin glycosylation.
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Affiliation(s)
- Kristiane Søreng
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
| | - Serhiy Pankiv
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
| | - Camilla Bergsmark
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
| | - Ellen M. Haugsten
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, 0379 Oslo, Norway
| | - Anette K. Dahl
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
| | - Laura R. de la Ballina
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
| | - Ai Yamamoto
- Department of Neurology, Pathology and Cell Biology, Columbia University, NY 10032-3784, USA
| | - Alf H. Lystad
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
| | - Anne Simonsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, 0379 Oslo, Norway
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3
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Giovannucci TA, Salomons FA, Stoy H, Herzog LK, Xu S, Qian W, Merino LG, Gierisch ME, Haraldsson M, Lystad AH, Uvell H, Simonsen A, Gustavsson AL, Vallin M, Dantuma NP. Identification of a novel compound that simultaneously impairs the ubiquitin-proteasome system and autophagy. Autophagy 2021; 18:1486-1502. [PMID: 34740308 PMCID: PMC9298443 DOI: 10.1080/15548627.2021.1988359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The ubiquitin-proteasome system (UPS) and macroautophagy/autophagy are the main proteolytic systems in eukaryotic cells for preserving protein homeostasis, i.e., proteostasis. By facilitating the timely destruction of aberrant proteins, these complementary pathways keep the intracellular environment free of inherently toxic protein aggregates. Chemical interference with the UPS or autophagy has emerged as a viable strategy for therapeutically targeting malignant cells which, owing to their hyperactive state, heavily rely on the sanitizing activity of these proteolytic systems. Here, we report on the discovery of CBK79, a novel compound that impairs both protein degradation by the UPS and autophagy. While CBK79 was identified in a high-content screen for drug-like molecules that inhibit the UPS, subsequent analysis revealed that this compound also compromises autophagic degradation of long-lived proteins. We show that CBK79 induces non-canonical lipidation of MAP1LC3B/LC3B (microtubule-associated protein 1 light chain 3 beta) that requires ATG16L1 but is independent of the ULK1 (unc-51 like autophagy activating kinase 1) and class III phosphatidylinositol 3-kinase (PtdIns3K) complexes. Thermal preconditioning of cells prevented CBK79-induced UPS impairment but failed to restore autophagy, indicating that activation of stress responses does not allow cells to bypass the inhibitory effect of CBK79 on autophagy. The identification of a small molecule that simultaneously impairs the two main proteolytic systems for protein quality control provides a starting point for the development of a novel class of proteostasis-targeting drugs.
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Affiliation(s)
- Tatiana A Giovannucci
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
| | - Florian A Salomons
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
| | - Henriette Stoy
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
| | - Laura K Herzog
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
| | - Shanshan Xu
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
| | - Weixing Qian
- Laboratories for Chemical Biology Umeå, Chemical Biology Consortium Sweden (CBCS), Umeå University, Umeå, Sweden
| | - Lara G Merino
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
| | - Maria E Gierisch
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
| | - Martin Haraldsson
- Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Alf H Lystad
- Department of Molecular Medicine, Institute of Basic Medical Sciences and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Blindern, Oslo, Norway
| | - Hanna Uvell
- Laboratories for Chemical Biology Umeå, Chemical Biology Consortium Sweden (CBCS), Umeå University, Umeå, Sweden
| | - Anne Simonsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Blindern, Oslo, Norway.,Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, Oslo, Norway
| | - Anna-Lena Gustavsson
- Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Michaela Vallin
- Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Nico P Dantuma
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
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4
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Munson MJ, Mathai BJ, Ng MYW, Trachsel-Moncho L, de la Ballina LR, Schultz SW, Aman Y, Lystad AH, Singh S, Singh S, Wesche J, Fang EF, Simonsen A. GAK and PRKCD are positive regulators of PRKN-independent mitophagy. Nat Commun 2021; 12:6101. [PMID: 34671015 DOI: 10.1101/2020.11.05.369496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 09/29/2021] [Indexed: 05/28/2023] Open
Abstract
The mechanisms involved in programmed or damage-induced removal of mitochondria by mitophagy remains elusive. Here, we have screened for regulators of PRKN-independent mitophagy using an siRNA library targeting 197 proteins containing lipid interacting domains. We identify Cyclin G-associated kinase (GAK) and Protein Kinase C Delta (PRKCD) as regulators of PRKN-independent mitophagy, with both being dispensable for PRKN-dependent mitophagy and starvation-induced autophagy. We demonstrate that the kinase activity of both GAK and PRKCD are required for efficient mitophagy in vitro, that PRKCD is present on mitochondria, and that PRKCD facilitates recruitment of ULK1/ATG13 to early autophagic structures. Importantly, we demonstrate in vivo relevance for both kinases in the regulation of basal mitophagy. Knockdown of GAK homologue (gakh-1) in C. elegans or knockout of PRKCD homologues in zebrafish led to significant inhibition of basal mitophagy, highlighting the evolutionary relevance of these kinases in mitophagy regulation.
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Affiliation(s)
- Michael J Munson
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway.
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway.
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
| | - Benan J Mathai
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
| | - Matthew Yoke Wui Ng
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
| | - Laura Trachsel-Moncho
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
| | - Laura R de la Ballina
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
| | - Sebastian W Schultz
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
- Department of Molecular Cell Biology, The Norwegian Radium Hospital Montebello, N-0379, Oslo, Norway
| | - Yahyah Aman
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, 1478, Lørenskog, Norway
| | - Alf H Lystad
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
| | - Sakshi Singh
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
| | - Sachin Singh
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
- Department of Tumor Biology, The Norwegian Radium Hospital Montebello, N-0379, Oslo, Norway
| | - Jørgen Wesche
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
- Department of Tumor Biology, The Norwegian Radium Hospital Montebello, N-0379, Oslo, Norway
| | - Evandro F Fang
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, 1478, Lørenskog, Norway
| | - Anne Simonsen
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway.
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway.
- Department of Molecular Cell Biology, The Norwegian Radium Hospital Montebello, N-0379, Oslo, Norway.
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5
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Munson MJ, Mathai BJ, Ng MYW, Trachsel-Moncho L, de la Ballina LR, Schultz SW, Aman Y, Lystad AH, Singh S, Singh S, Wesche J, Fang EF, Simonsen A. GAK and PRKCD are positive regulators of PRKN-independent mitophagy. Nat Commun 2021; 12:6101. [PMID: 34671015 PMCID: PMC8528926 DOI: 10.1038/s41467-021-26331-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 09/29/2021] [Indexed: 12/26/2022] Open
Abstract
The mechanisms involved in programmed or damage-induced removal of mitochondria by mitophagy remains elusive. Here, we have screened for regulators of PRKN-independent mitophagy using an siRNA library targeting 197 proteins containing lipid interacting domains. We identify Cyclin G-associated kinase (GAK) and Protein Kinase C Delta (PRKCD) as regulators of PRKN-independent mitophagy, with both being dispensable for PRKN-dependent mitophagy and starvation-induced autophagy. We demonstrate that the kinase activity of both GAK and PRKCD are required for efficient mitophagy in vitro, that PRKCD is present on mitochondria, and that PRKCD facilitates recruitment of ULK1/ATG13 to early autophagic structures. Importantly, we demonstrate in vivo relevance for both kinases in the regulation of basal mitophagy. Knockdown of GAK homologue (gakh-1) in C. elegans or knockout of PRKCD homologues in zebrafish led to significant inhibition of basal mitophagy, highlighting the evolutionary relevance of these kinases in mitophagy regulation.
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Affiliation(s)
- Michael J Munson
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway.
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway.
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
| | - Benan J Mathai
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
| | - Matthew Yoke Wui Ng
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
| | - Laura Trachsel-Moncho
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
| | - Laura R de la Ballina
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
| | - Sebastian W Schultz
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
- Department of Molecular Cell Biology, The Norwegian Radium Hospital Montebello, N-0379, Oslo, Norway
| | - Yahyah Aman
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, 1478, Lørenskog, Norway
| | - Alf H Lystad
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
| | - Sakshi Singh
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
| | - Sachin Singh
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
- Department of Tumor Biology, The Norwegian Radium Hospital Montebello, N-0379, Oslo, Norway
| | - Jørgen Wesche
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
- Department of Tumor Biology, The Norwegian Radium Hospital Montebello, N-0379, Oslo, Norway
| | - Evandro F Fang
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, 1478, Lørenskog, Norway
| | - Anne Simonsen
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway.
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway.
- Department of Molecular Cell Biology, The Norwegian Radium Hospital Montebello, N-0379, Oslo, Norway.
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6
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Durgan J, Lystad AH, Sloan K, Carlsson SR, Wilson MI, Marcassa E, Ulferts R, Webster J, Lopez-Clavijo AF, Wakelam MJ, Beale R, Simonsen A, Oxley D, Florey O. Non-canonical autophagy drives alternative ATG8 conjugation to phosphatidylserine. Mol Cell 2021; 81:2031-2040.e8. [PMID: 33909989 PMCID: PMC8122138 DOI: 10.1016/j.molcel.2021.03.020] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 01/15/2021] [Accepted: 03/16/2021] [Indexed: 01/22/2023]
Abstract
Autophagy is a fundamental catabolic process that uses a unique post-translational modification, the conjugation of ATG8 protein to phosphatidylethanolamine (PE). ATG8 lipidation also occurs during non-canonical autophagy, a parallel pathway involving conjugation of ATG8 to single membranes (CASM) at endolysosomal compartments, with key functions in immunity, vision, and neurobiology. It is widely assumed that CASM involves the same conjugation of ATG8 to PE, but this has not been formally tested. Here, we discover that all ATG8s can also undergo alternative lipidation to phosphatidylserine (PS) during CASM, induced pharmacologically, by LC3-associated phagocytosis or influenza A virus infection, in mammalian cells. Importantly, ATG8-PS and ATG8-PE adducts are differentially delipidated by the ATG4 family and bear different cellular dynamics, indicating significant molecular distinctions. These results provide important insights into autophagy signaling, revealing an alternative form of the hallmark ATG8 lipidation event. Furthermore, ATG8-PS provides a specific "molecular signature" for the non-canonical autophagy pathway.
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Affiliation(s)
- Joanne Durgan
- Signalling Programme, Babraham Institute, Cambridge, UK
| | - Alf H Lystad
- Department of Molecular Medicine, University of Oslo, Oslo, Norway
| | | | - Sven R Carlsson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | | | | | | | - Judith Webster
- Mass Spectrometry Facility, Babraham Institute, Cambridge, UK
| | | | - Michael J Wakelam
- Signalling Programme, Babraham Institute, Cambridge, UK; Lipidomics Facility, Babraham Institute, Cambridge, UK
| | | | - Anne Simonsen
- Department of Molecular Medicine, University of Oslo, Oslo, Norway
| | - David Oxley
- Mass Spectrometry Facility, Babraham Institute, Cambridge, UK
| | - Oliver Florey
- Signalling Programme, Babraham Institute, Cambridge, UK.
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7
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Melia TJ, Lystad AH, Simonsen A. Autophagosome biogenesis: From membrane growth to closure. J Cell Biol 2021; 219:151729. [PMID: 32357219 PMCID: PMC7265318 DOI: 10.1083/jcb.202002085] [Citation(s) in RCA: 146] [Impact Index Per Article: 48.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/04/2020] [Accepted: 04/06/2020] [Indexed: 12/14/2022] Open
Abstract
Autophagosome biogenesis involves de novo formation of a membrane that elongates to sequester cytoplasmic cargo and closes to form a double-membrane vesicle (an autophagosome). This process has remained enigmatic since its initial discovery >50 yr ago, but our understanding of the mechanisms involved in autophagosome biogenesis has increased substantially during the last 20 yr. Several key questions do remain open, however, including, What determines the site of autophagosome nucleation? What is the origin and lipid composition of the autophagosome membrane? How is cargo sequestration regulated under nonselective and selective types of autophagy? This review provides key insight into the core molecular mechanisms underlying autophagosome biogenesis, with a specific emphasis on membrane modeling events, and highlights recent conceptual advances in the field.
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Affiliation(s)
- Thomas J Melia
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
| | - Alf H Lystad
- Department of Molecular Medicine, Institute of Basic Medical Sciences and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anne Simonsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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8
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Dragich JM, Kuwajima T, Hirose-Ikeda M, Yoon MS, Eenjes E, Bosco JR, Fox LM, Lystad AH, Oo TF, Yarygina O, Mita T, Waguri S, Ichimura Y, Komatsu M, Simonsen A, Burke RE, Mason CA, Yamamoto A. Autophagy linked FYVE (Alfy/WDFY3) is required for establishing neuronal connectivity in the mammalian brain. eLife 2016; 5. [PMID: 27648578 PMCID: PMC5030082 DOI: 10.7554/elife.14810] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 08/25/2016] [Indexed: 12/23/2022] Open
Abstract
The regulation of protein degradation is essential for maintaining the appropriate environment to coordinate complex cell signaling events and to promote cellular remodeling. The Autophagy linked FYVE protein (Alfy), previously identified as a molecular scaffold between the ubiquitinated cargo and the autophagic machinery, is highly expressed in the developing central nervous system, indicating that this pathway may have yet unexplored roles in neurodevelopment. To examine this possibility, we used mouse genetics to eliminate Alfy expression. We report that this evolutionarily conserved protein is required for the formation of axonal tracts throughout the brain and spinal cord, including the formation of the major forebrain commissures. Consistent with a phenotype reflecting a failure in axon guidance, the loss of Alfy in mice disrupts localization of glial guidepost cells, and attenuates axon outgrowth in response to Netrin-1. These findings further support the growing indication that macroautophagy plays a key role in the developing CNS.
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Affiliation(s)
- Joanna M Dragich
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, United States
| | - Takaaki Kuwajima
- Department of Pathology, College of Physicians and Surgeons, Columbia University, New York, United States.,Department of Cell Biology, College of Physicians and Surgeons, Columbia University, New York, United States
| | - Megumi Hirose-Ikeda
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, United States
| | - Michael S Yoon
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, United States
| | - Evelien Eenjes
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, United States
| | - Joan R Bosco
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, United States
| | - Leora M Fox
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, United States.,Doctoral Program in Neurobiology and Behavior, Columbia University, New York, United States
| | - Alf H Lystad
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Tinmarla F Oo
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, United States
| | - Olga Yarygina
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, United States
| | - Tomohiro Mita
- The Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Satoshi Waguri
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Yoshinobu Ichimura
- The Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Masaaki Komatsu
- The Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Anne Simonsen
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Robert E Burke
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, United States.,Department of Pathology, College of Physicians and Surgeons, Columbia University, New York, United States.,Department of Cell Biology, College of Physicians and Surgeons, Columbia University, New York, United States
| | - Carol A Mason
- Department of Pathology, College of Physicians and Surgeons, Columbia University, New York, United States.,Department of Cell Biology, College of Physicians and Surgeons, Columbia University, New York, United States.,Department of Neuroscience, College of Physicians and Surgeons, Columbia University, New York, United States.,Department of Ophthalmology, College of Physicians and Surgeons, Columbia University, New York, United States
| | - Ai Yamamoto
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, United States.,Department of Pathology, College of Physicians and Surgeons, Columbia University, New York, United States.,Department of Cell Biology, College of Physicians and Surgeons, Columbia University, New York, United States
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